ideal-genome-qc documentation

ideal-genom-qc is a Python library for performing automated and reproducible quality control (QC) on genomic data, with a focus on ancestry, variant filtering, and sample-level QC. It is designed to integrate with modern bioinformatics tools and supports visualizations and report generation.

Features

• Sample, Ancestry and Variant QC pipelines

• Additional population structure analysis using PCA and UMAP

• Full automated pipeline for QC

• Many plots to report the results

• Clean API and extensible modules

Installation

You can install the latest version from PyPI:

pip install ideal-genom-qc

Or clone the repository and install it locally: (Disclaimer: this version could have some errors because contains the latest changes)

git clone https://github.com/cge-tubingens/IDEAL-GENOM-QC.git

Documentation

• ideal_genom_qc.SampleQC
  • SampleQC
• ideal_genom_qc.AncestryQC
  • AncestryQC
  • GenomicOutlierAnalyzer
  • ReferenceGenomicMerger
• ideal_genom_qc.UMAPplot
  • UMAPplot
• ideal_genom_qc.VariantQC
  • VariantQC
• ideal_genom_qc.Helpers
  • arg_parser()
  • delete_temp_files()
  • shell_do()
• ideal_genom_qc.get_references
  • Fetcher1000Genome
  • FetcherLDRegions